[gmx-users] trjconv in martini

[mohammad agha]

Dear gromacs users,

At the first I thank from Tsjerk and Mark because of their answers to me but unfortunately I don't understand that where is my mistake, still?

I work with MARTINI coarse-grained and I have a problem after -pbc nojump! My simulation lasts 600 ns and 2 micelles are created from 200 ns and 
remain during 400 ns, then my micelles isn't formed at the end of the trajectory.
My commands are:
1- trjconv -f md.trr -s md.tpr -n index.ndx -e 600000 -pbc cluster -o 1.gro
 In this step I viewed 2 micelles from 200 ns to 600 ns by ngmx -f 1.gro -s md.tpr, so I have 2 micelles and -pbc cluster works me well and has been removed box boundaries from my system but I saw very jumps in my system. Okay?

2- grompp -f md.mdp -c 1.gro -o 1.tpr -n index.ndx
3- trjconv -f 1.gro -s 1.tpr -o 2.xtc -pbc nojump
After this step, had been removed jumps but I didn't see 2 micelles in 200 ns, I saw that my monomers were collected as groups in the different places. (This is bad and I don't know where is my mistake and what should I do to solve my problem!)
After this, to solve my problem, I did:
4- trjconv -f 2.xtc -s 1.tpr -o 3.xtc -pbc mol

In this step, I viewed 2 micelles from 200 ns to 600 ns and had been removed jumps but existed boundaries of box, means my micelles that leaves a simulation box by, say, the right-hand face, then enters the simulation box by the left-hand face. 

May I know can I start analysis of my system with 3.xtc? Is it good? If it isn't good, Please help me for this problem with nojump.

Thank you very much in advance
Best Regards
Sara
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